BN1317 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 9.7243e-09 1.0864e-06
Layer 3 1.7942e-08 1.2980e-06
Layer 2 5.2533e-08 4.8807e-07
Layer 5 2.6419e-05 2.3698e-04
Layer 6 5.7663e-05 1.0786e-03
WM 1.4438e-02 2.9344e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
GABARAP Expression Distribution
Gene Specificity Score (GSS)
GABARAP GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
GABARAP Layer 3 4.4688 0.8941
GLUL Layer 2 4.8418 0.8892
FXYD1 Layer 2 5.7969 0.8885
TMBIM6 Layer 3 4.2734 0.8867
METRN Layer 2 4.5352 0.8867
NTRK2 Layer 2 4.5508 0.8864
PRDX1 Layer 2 4.5156 0.8852
SOD1 Layer 4 4.7656 0.8851
SPTBN1 Layer 4 4.8301 0.8850
HSPB1 Layer 3 4.6133 0.8847
ATP1A2 Layer 2 5.3477 0.8843
MT1M Layer 2 5.4375 0.8842
CD81 Layer 3 4.2617 0.8841
ELOB Layer 2 4.4258 0.8838
COX6A1 Layer 4 4.7422 0.8838
RPL5 Layer 2 4.0156 0.8832
ELAVL3 Layer 2 4.2617 0.8828
RPL14 Layer 2 4.3906 0.8822
PPP1R1B Layer 4 4.6445 0.8820
ALDOC Layer 3 4.9102 0.8819
ITM2B Layer 4 4.5078 0.8818
AHCYL1 Layer 2 4.3223 0.8817
NDUFA3 Layer 4 4.3867 0.8810
TSPAN7 Layer 4 6.2461 0.8809
TUBB2B Layer 2 5.3477 0.8806
C1orf61 Layer 2 4.9609 0.8805
IFI6 Layer 2 4.7422 0.8805
COX8A Layer 2 4.9727 0.8804
COX4I1 Layer 4 4.4688 0.8804
COPS9 Layer 2 4.8789 0.8803
AGT Layer 2 4.2539 0.8794
NDUFA1 Layer 3 4.4102 0.8789
SNHG6 Layer 3 4.2812 0.8784
RPS15A Layer 3 4.0586 0.8783
KIF5A Layer 3 5.4961 0.8782
UQCR11 Layer 4 4.8828 0.8781
RPS4X Layer 2 3.9883 0.8781
NDUFAF8 Layer 2 3.5215 0.8779
SRP14 Layer 2 4.3691 0.8779
LINC00632 Layer 2 4.8555 0.8778
SLC1A3 Layer 2 5.6523 0.8773
BSG Layer 3 4.6523 0.8773
LMO4 Layer 4 5.1328 0.8769
NDUFS5 Layer 4 4.3965 0.8768
GPX4 Layer 4 4.5664 0.8766
HSPA8 Layer 2 4.5996 0.8763
ENHO Layer 4 4.1230 0.8758
HOPX Layer 2 6.2617 0.8753
HNRNPDL Layer 4 4.0156 0.8753
YWHAE Layer 4 4.3906 0.8753

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1317
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1317_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1317/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1317/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1317/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1317/report/PD/BN1317_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1317/report/PD/BN1317_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 03:22:51
  • Number of Processes: 10
  • Spending Time: 0h 3m